bioRxiv

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multiDEGGs: a multi-omic differential network analysis package for biomarker discovery and predictive modeling

bioRxiv Jan 1, 2025
Modern clinical trials increasingly leverage high-throughput omic data for patient stratification and biomarker discovery. While traditional differential gene expression analysis disregards the networked nature of molecular entities and produces exte...
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Human-scATAC-Corpus: a comprehensive database of scATAC-seq data

bioRxiv Jan 1, 2025
Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) profiles chromatin accessibility at cellular resolution, making it possible to reveal epigenomic landscapes that govern gene regulation in a variety of cells. Nevert...
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CoBRA: Compound Binding Site Prediction using RNA Language Model

bioRxiv Jan 1, 2025
Ribonucleic acid (RNA) molecules perform a variety of functions within cells and thus implicated in various human diseases such as cancer. The fact that the proteins constitute a small portion of mRNAs and the ability of RNA to form highly specific t...
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Deep Learning Driven Investigation of Nanoplastic Impacts on Soil Protist Behavior in Soil Chips

bioRxiv Jan 1, 2025
Nanoplastics are emerging contaminants that have a significant impact on soil microorganisms. To fully understand the effect of plastic contamination on soil ecosystems, it is necessary to advance techniques that can monitor nanoplastic-microbe inter...
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Alzheimer’s subtypes A supervised, unsupervised, multimodal, multilayered embedded recursive (SUMMER) AI study

bioRxiv Jan 1, 2025
Since Alzheimer’s disease (AD) is a heterogeneous disease, different subtypes may have distinct biological, genetic, and clinical characteristics, requiring tailored interventions. While several proposed subtypes of AD exist, there is still no clear ...
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Design and Implementation of a Decision Making System for Controlling a Hand Exoskeleton Based on EEG/EMG Signals

bioRxiv Jan 1, 2025
This paper presents an approach of combining Electroencephalography (EEG) and Electromyography (EMG) signals to create a hybrid Brain Interface Computer (BCI) device for controlling a hand exoskeleton through classifying the flexion attempt and resti...
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Satiation is associated with OGT-dependent regulation of excitatory synapses

bioRxiv Jan 1, 2025
Satiation is essential for energy homeostasis and is dysregulated in metabolic disorders like obesity and eating disorders such as anorexia nervosa. While satiation engages a large neural network across brain regions, how the communication within thi...
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Structure-based discovery of inhibitors of Mac1 domain of nonstructural protein-3 of SARS-CoV-2 by machine learning-augmented screening of chemical space

bioRxiv Jan 1, 2025
Significant efforts have been recently dedicated to the discovery of small molecule inhibitors against the Macrodomain 1 (Mac1) of nonstructural protein 3 (NSP3) as potential antivirals for SARS-CoV-2. Thus, Mac1 has also been selected as the target ...
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scXpand: Pan-cancer detection of T-cell clonal expansion from single-cell RNA sequencing without paired single-cell TCR sequencing

bioRxiv Jan 1, 2025
Advances in single-cell sequencing have enabled detailed characterization of T-cell clonal dynamics in cancer. However, analyses aiming to link transcriptional landscape to T-cell clonality remain limited by confounding factors unequally controlled i...
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Large Language Models Reveal the Neural Tracking of Linguistic Context in Attended and Unattended Multi-Talker Speech

bioRxiv Jan 1, 2025
Large language models (LLMs) have shown strong alignment with contextualized semantic encoding in the brain, offering a new avenue for studying language processing. However, natural speech often occurs in multi-talker environments, which remain under...
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